scholarly journals Missed opportunities in large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Damjan Krstajic
Keyword(s):  
Drug Discovery ◽  
Ligand Binding ◽  
Large Scale ◽  
Prediction Methods ◽  
Missed Opportunities ◽  
Conformal Prediction

Abstract Recently Bosc et al. (J Cheminform 11(1): 4, 2019), published an article describing a case study that directly compares conformal predictions with traditional QSAR methods for large-scale predictions of target-ligand binding. We consider this study to be very important. Unfortunately, we have found several issues in the authors’ approach as well as in the presentation of their findings.

scholarly journals Reply to “Missed opportunities in large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery”

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Nicolas Bosc ◽  
Francis Atkinson ◽  
Eloy Félix ◽  
Anna Gaulton ◽  
Anne Hersey ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Scientific Community ◽  
Large Scale ◽  
Prediction Methods ◽  
Missed Opportunities ◽  
Conformal Prediction ◽  
Letter To The Editor ◽  
Published Paper

Abstract In response to Krstajic’s letter to the editor concerning our published paper, we here take the opportunity to reply, to re-iterate that no errors in our work were identified, to provide further details, and to re-emphasise the outputs of our study. Moreover, we highlight that all of the data are freely available for the wider scientific community (including the aforementioned correspondent) to undertake follow-on studies and comparisons.

scholarly journals Large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Nicolas Bosc ◽  
Francis Atkinson ◽  
Eloy Felix ◽  
Anna Gaulton ◽  
Anne Hersey ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Large Scale ◽  
Prediction Methods ◽  
Conformal Prediction

scholarly journals Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Ulf Norinder ◽  
Ola Spjuth ◽  
Fredrik Svensson
Keyword(s):  
Decision Making ◽  
Drug Discovery ◽  
Large Scale ◽  
Predictive Performance ◽  
Training Data ◽  
Conformal Prediction ◽  
Valuable Addition ◽  
Conformal Predictors ◽  
Data Synergy ◽  
Training Sets

AbstractConfidence predictors can deliver predictions with the associated confidence required for decision making and can play an important role in drug discovery and toxicity predictions. In this work we investigate a recently introduced version of conformal prediction, synergy conformal prediction, focusing on the predictive performance when applied to bioactivity data. We compare the performance to other variants of conformal predictors for multiple partitioned datasets and demonstrate the utility of synergy conformal predictors for federated learning where data cannot be pooled in one location. Our results show that synergy conformal predictors based on training data randomly sampled with replacement can compete with other conformal setups, while using completely separate training sets often results in worse performance. However, in a federated setup where no method has access to all the data, synergy conformal prediction is shown to give promising results. Based on our study, we conclude that synergy conformal predictors are a valuable addition to the conformal prediction toolbox.

A Family With Autosomal-Dominant Progressive Sensorineural Hearing Loss

1996 ◽  
Vol 5 (1) ◽  
pp. 23-32 ◽  
Author(s):  
Chris Halpin ◽  
Barbara Herrmann ◽  
Margaret Whearty
Keyword(s):  
Speech Production ◽  
Hearing Aids ◽  
Role Models ◽  
Speech Intelligibility ◽  
Large Scale ◽  
Speech Language Pathology ◽  
The Family ◽  
Patient Will ◽  
Language Pathology

The family described in this article provides an unusual opportunity to relate findings from genetic, histological, electrophysiological, psychophysical, and rehabilitative investigation. Although the total number evaluated is large (49), the known, living affected population is smaller (14), and these are spread from age 20 to age 59. As a result, the findings described above are those of a large-scale case study. Clearly, more data will be available through longitudinal study of the individuals documented in the course of this investigation but, given the slow nature of the progression in this disease, such studies will be undertaken after an interval of several years. The general picture presented to the audiologist who must rehabilitate these cases is that of a progressive cochlear degeneration that affects only thresholds at first, and then rapidly diminishes speech intelligibility. The expected result is that, after normal language development, the patient may accept hearing aids well, encouraged by the support of the family. Performance and satisfaction with the hearing aids is good, until the onset of the speech intelligibility loss, at which time the patient will encounter serious difficulties and may reject hearing aids as unhelpful. As the histological and electrophysiological results indicate, however, the eighth nerve remains viable, especially in the younger affected members, and success with cochlear implantation may be expected. Audiologic counseling efforts are aided by the presence of role models and support from the other affected members of the family. Speech-language pathology services were not considered important by the members of this family since their speech production developed normally and has remained very good. Self-correction of speech was supported by hearing aids and cochlear implants (Case 5’s speech production was documented in Perkell, Lane, Svirsky, & Webster, 1992). These patients received genetic counseling and, due to the high penetrance of the disease, exhibited serious concerns regarding future generations and the hope of a cure.

The Boeing 787 Dreamliner--A case study in large-scale design integration

2008 ◽  
Author(s):  
D. L. McMullin ◽  
A. R. Jacobsen ◽  
D. C. Carvan ◽  
R. J. Gardner ◽  
J. A. Goegan ◽  
...  
Keyword(s):  
Large Scale ◽  
Design Integration ◽  
Scale Design

Disruptive innovation and operationalization in local and sustainable food systems: Examining the University of Toronto-Local Food Plus partnership

2019 ◽  
Vol 6 (1) ◽  
pp. 120-139
Author(s):  
Lori Stahlbrand
Keyword(s):  
Food Systems ◽  
Large Scale ◽  
Food System ◽  
Local Food ◽  
Disruptive Innovation ◽  
Government Support ◽  
Sustainable Food ◽  
University Of Toronto ◽  
The University

This paper traces the partnership between the University of Toronto and the non-profit Local Food Plus (LFP) to bring local sustainable food to its St. George campus. At its launch, the partnership represented the largest purchase of local sustainable food at a Canadian university, as well as LFP’s first foray into supporting institutional procurement of local sustainable food. LFP was founded in 2005 with a vision to foster sustainable local food economies. To this end, LFP developed a certification system and a marketing program that matched certified farmers and processors to buyers. LFP emphasized large-scale purchases by public institutions. Using information from in-depth semi-structured key informant interviews, this paper argues that the LFP project was a disruptive innovation that posed a challenge to many dimensions of the established food system. The LFP case study reveals structural obstacles to operationalizing a local and sustainable food system. These include a lack of mid-sized infrastructure serving local farmers, the domination of a rebate system of purchasing controlled by an oligopolistic foodservice sector, and embedded government support of export agriculture. This case study is an example of praxis, as the author was the founder of LFP, as well as an academic researcher and analyst.

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